Postdoctoral Researcher

University of Chile

Santiago, Chile

Present - Apr. 2021

• Fondecyt postdoctoral research grant: Linguistic characterization of the Chilean clinical text: towards an automatic extraction of information

Ph.D. in Biomedical Sciences

University of Chile

Santiago, Chile

Jan. 2018 - Mar. 2013

• Thesis: Genetic linkage and association analysis to identify genetic risk markers of cholelithiasis and gallbladder cancer in Chile.

M.S. in Biological Sciences, mention in Genetics

University of Chile

Santiago, Chile

Jun. 2013 - Apr. 2011

• Thesis: Role of the TRPM4 channel in the development of prostate cancer in a transgenic murine model.

B.S. Microbiology and Bioanalysis

University of Antioquia

Medellín, Colombia

May. 2009 - Jan. 2003

Researcher

Center for Mathematical Modeling, University of Chile

Santiago, Chile

Jul. 2021 - Jan. 2021

• Named entity recognition of tumor morphology and topography from surgical pathology reports.
• PI: Jocelyn Dunstan

Researcher

Center for Medical Informatics and Telemedicine, University of Chile

Santiago, Chile

Mar. 2021 - Jan. 2020

• Automatic analysis of clinical narratives produced in Chile using neural networks.
• PI: Jocelyn Dunstan

Researcher

Center for Medical Informatics and Telemedicine, University of Chile

Santiago, Chile

Dec. 2020 - Dec. 2019

• FONDEF IDeA I+D 2019 (2019-2021): “Deep-Pathology: Distributed TelePathology Platform Based on Blockchain and Collaborative Diagnosis Supported by Deep Learning”.
• PI: Steffen Härtel Gründler

Postdoctoral Researcher

Center for Medical Informatics and Telemedicine, University of Chile

Santiago, Chile

Dec 2019 - Sep. 2018

• Systematic analysis of family history in free text of electronic medical records.

PhD Candidate

Foundation for Advanced Biomedical Studies (FEBA), Faculty of Medicine, University of Chile

Santiago, Chile

Apr. 2018 - Dec. 2017

• Analysis of germline and somatic genetic variants in patients with gallbladder cancer.

PhD Student - Candidate

Cancer Genomics Laboratory, Faculty of Medicine, University of Chile

Santiago, Chile

Jan. 2018 - Aug. 2014

• Statistical analysis of socio-demographic information
• Genetic linkage analysis in families with multiple gallbladder cancer patients
• Fine mapping and genome wide association analysis in a case-control study

Graduate Student Fellow

Institute of Medical Biometry and Informatics (IMBI), University Hospital Heidelberg

Heidelberg, Germany

Feb. 2016 - Aug. 2015

• Trained in specialized bioinformatics tools (R, PLINK and Mendel) to analyze genetic data
• Attended the EMBL Conference: Cancer Genomics
• Attended scientific talks organized by the University of Heidelberg and the German Center for Oncological Research (dkfz)

Master’s student

Laboratory of Molecular Cancer Pathology, Faculty of Medicine, University of Chile

Santiago, Chile

Jun. 2013 - Mar. 2012

• Histopathological analysis of prostate, lymph nodes and lung sections of a murine model of prostate cancer (TRAMP mice)
• Quantification of mRNA using real-time RT-PCR on TRAMP mice prostates

Diagnosis Foundation

Advisory member of the Diagnosis Foundation

Santiago, Chile

Dec. 2021 - Nov. 2019

• Support the diagnosis and research of unknown diseases
• Promote the knowledge generation through ethical and collaborative scientific research

Undergraduate Teaching - Coordinating Professor

School of Medical Technology, Universidad del Desarrollo

Santiago, Chile

Present - Sep. 2023

• CB. Medical Informatics
• Course of the formative area of the Clinical Bioanalysis, Hematology and Blood Bank specialty, with 68 academic hours taught in the eighth semester of the Study Plan.

Undergraduate Methodological Advisor

School of Medical Technology, Universidad del Desarrollo

Santiago, Chile

Present - Sep. 2023

• Research Seminar

Graduate Teaching - Coordinating Professor

International Master in Medical Informatics, University of Chile

Santiago, Chile

Present - Aug. 2020

• CA. Bioinformatics I and II

Undergraduate Teaching - Coordinating Professor

School of Medical Technology, Universidad del Desarrollo

Santiago, Chile

Present - Aug. 2021

• CB. Bioinformatics in Molecular Diagnostics
• Course of the formative area of the Morphophysiopathology and Cytodiagnosis specialty, with 102 academic hours taught in the eighth semester of the Study Plan

Master Thesis Supervisor

International Master in Medical Informatics, University of Chile

Santiago, Chile

Jun. 2022 - Jul. 2021

• Automatic Staging of Distant Metastases in Imaging Reports Using Natural Language Processing
• Ricardo Ahumada’s Master Thesis Supervisor together with Jocelyn Dunstan PhD

Master Thesis Examiner

International Master in Medical Informatics, University of Chile

Santiago, Chile

Apr. 2022 - Jul. 2021

• Automatic transcription and extraction of key information from Spanish-language clinical audios
• Maicol Fernandez’s Master Thesis Examiner

Graduate Teaching - Guest Professor

International Master in Medical Informatics, University of Chile

Santiago, Chile

Jun. 2021

• CA. Statistical Analysis Methods II
• Language Resources Creation for NLP

Graduate Teaching - Guest Professor

International Master in Medical Informatics, University of Chile

Santiago, Chile

Jul. 2020 - May. 2020

• CB. Biostatistics I and II

Undergraduate Student Supervisor

Faculty of Medicine, University of Chile

Santiago, Chile

Dec. 2020 - Mar. 2020

• Research Unit I and II
• 40 hour tutoring of second-year medical students
• Guidance on the construction and execution of a short research project

Graduate Teaching - Guest Professor

International Master in Medical Informatics, University of Chile

Santiago, Chile

Oct. 2018

• CA. Biomedicine II
• Genetic epidemiology studies in cancer

Undergraduate Teaching - Guest Professor

School of Medical Technology, Universidad del Desarrollo

Santiago, Chile

Oct. 2018 - Aug. 2018

• CB. Scientific Bases of Medical Technology

Undergraduate Teaching - Guest Professor

School of Medical Technology, Universidad Mayor

Santiago, Chile

Sep. 2017

• CB. Applied Biotechnology

Undergraduate Student Supervisor

Faculty of Medicine, University of Chile

Santiago, Chile

Jan. 2017 - Mar. 2016

• Research Unit I and II
• 40 hour tutoring of second-year medical students
• Guidance on the construction and execution of a short research project

Undergraduate Teaching - Auxiliary Guest Professor

School of Medical Technology, ICBM, University of Chile

Santiago, Chile

May. 2015

• Seminars on the application of Molecular Biology

E-Learning Module for Cytopathology Education Based on Virtual Microscopy

Journal of the American Society of Cytopathology

Santiago, Chile

2023

• Cubillos, L., Diaz, E., Báez, P., Gutiérrez, L., Molina C., Härtel, S.
• (in press)

Amerindian Ancestry Proportion as a Risk Factor for Inflammatory Bowel Diseases: Results from a Latin American Andean Cohort

Frontiers in Medicine

Santiago, Chile

2023

• Pérez-Jeldres, T., Magne, F., Ascui, G., Alvares D., Orellana, M., Álvarez-Lobos, M., Hernández-Rocha, C., Azócar, L., Aguilar, N., Espino, A., Estela, R., Escobar, S., Zazueta, A., Baez, P., Silva, V., De La Vega, A., Arriagada, E., Pavez-Ovalle, C., Diaz-Asencio, A., Travisany, D., … Bustamante, M.L.
• (in press)

Genotype Prevalence of Lactose Deficiency, Vitamin D Deficiency, and the Vitamin D Receptor in a Chilean Inflammatory Bowel Disease Cohort: Insights from an Observational Study

International Journal of Molecular Sciences

Santiago, Chile

2023

• Pérez-Jeldres, T., Bustamante, M. L., Segovia-Melero, R., Aguilar, N., Magne, F., Ascui, G., Uribe, D., Azócar, L., Hernández-Rocha, C., Estela, R., Silva, V., De La Vega, A., Arriagada, E., Gonzalez, M., Onetto, G.-F., Escobar, S., Baez, P., Zazueta, A., Pavez-Ovalle, C., … Álvarez-Lobos, M.
• 

Genome sequencing reveals molecular subgroups in oral epithelial dysplasia

Brazilian Oral Research

Santiago, Chile

2023

• Márquez A., Mujica I., Jordan N., Báez P., Tarquinio S., Nunes J., Adorno D., Martínez B., Morales-Pison S., Fernandez-Ramires R.
• 

Natural language processing for clinical text in Spanish: The case of waiting lists in Chile

Revista Médica Clínica Las Condes, 2022, vol. 33, no 6, p. 576-582.

Santiago, Chile

2022

• Báez, P., Arancibia, A. P., Chaparro, M. I., Bucarey, T., Núñez, F., & Dunstan, J.
• 

Ethnicity influences phenotype and clinical outcomes: Comparing a South American with a North American inflammatory bowel disease cohort

Medicine, September 09, 2022 - Volume 101 - Issue 36 - p e30216

Santiago, Chile

2022

• Pérez-Jeldres T, Pizarro B, Ascui G, Orellana M, Cerda-Villablanca M, Alvares D, De La Vega A, Cannistra M, Cornejo B, Báez P, Silva V, Arriagada E, Rivera-Nieves J, Estela R, Hernández-Rocha C, Álvarez- Lobos M, Tobar F.
• 

Cáncer de vesícula en colecistectomías de la región de Tarapacá. Análisis según pertenencia étnica

Revista Médica de Chile, 150(9).

Santiago, Chile

2022

• Fonseca C, M., García R, J., Csendes J, A., Calcagno Z, S., Ibaceta O, D., Báez B, P., & Marcelain C, K.
• 

Automatic support system for tumor coding in pathology reports in Spanish

Preprint available at SSRN 3982259

Santiago, Chile

2022

• Villena, F., Báez, P., Peñafiel, S., Rojas, M. & Dunstan, J.
• 

Automatic Extraction of Nested Entities in Clinical Referrals in Spanish

ACM Transactions on Computing for Healthcare (HEALTH), 2022, vol. 3, no 3, p. 1-22.

Santiago, Chile

2022

• Báez, P., Bravo-Marquez, F., Dunstan, J., Rojas, M. & Villena, F.
• 

Construcción de recursos de texto para la identificación automática de información clínica en narrativas no estructuradas

Revista Médica de Chile, 149(7).

Santiago, Chile

2021

• Báez, P., Villena, F., Zúñiga K., Jones N., Fernández G., Durán, M. & Dunstan, J.
• 

Prevalencia de colecistolitiasis y cáncer de vesícula en una población rural Aymara de Chile

Revista Médica de Chile, 148(10).

Santiago, Chile

2020

• Fonseca C, M., Baéz B, P., Csendes J, A., Calcagno Z, S., Marcelain C, K., Vargas M, P., García R, J., & Barlaro F, T.
• 

The Chilean Waiting List Corpus: a new resource for Clinical Named Entity Recognition

Proceedings of the 3rd Clinical Natural Language Processing Workshop (pp. 291-300)

Santiago, Chile

2020

• Báez, P., Villena, F., Rojas, M., Durán, M., & Dunstan, J.
• Best Paper Session at the 3rd Clinical NLP Workshop - EMNLP Conference 2020
• 

ABCB1/4 Gallbladder Cancer Risk Variants Identified in India Also Show Strong Effects in Chileans

Cancer Epidemiol. 2020 Apr;65:101643.

Santiago, Chile

2020

• Boekstegers F., Marcelain K., Barahona C., Báez P., Müller B., et al.
• 

TRPM4 regulates Akt/GSK3-β activity and enhances β-catenin signaling and cell proliferation in prostate cancer cells

Mol Oncol. 2018 Feb; 12(2):151-165.

Santiago, Chile

2018

• Sagredo, A. I., Sagredo, E. A., Cappelli, C., Báez, P., Rodrigo, A. M., et al.
• 

Subtypes of Native American ancestry and leading causes of death: Mapuche ancestry-specific associations with gallbladder cancer risk in Chile

PLoS Genet 13(5): e1006756.

Santiago, Chile

2017

• Lorenzo Bermejo J, Boekstegers F, González Silos R, Marcelain K, Báez P., et al.
• 

Mast Cell Infiltration and Kit and Protease Expression During Progression of a Transgenic Prostate Cancer Murine Model (TRAMP)

Journal of Comparative Pathology, 150(1), 88.

Santiago, Chile

2014

• González, C., Armisén, R., Stutzin, A., Baez, P., Landerer, E., Paredes, R., Contreras, I., Muñoz, C.

Actualización en cáncer de próstata: generalidades y diagnóstico

Medicina & Laboratorio, 18, 7-8.

Santiago, Chile

2012

• Báez, P., Armisén Yañez, R.

Colonización por Staphylococcus aureus resistente a meticilina en las manos de individuos de la comunidad

Iatreia, 23(1), 5-9.

Medellín, Colombia

2010

• Báez, P., Zapata Tamayo, M., Ramírez Pérez, A., Rúa Giraldo, A., & Jiménez Quiceno, J.

Fondecyt Postdoctoral Research Grant

National Agency for Research and Development - ANID

Santiago, Chile

Apr. 2021

Best Paper

3rd Clinical Natural Language Processing Workshop. Paper title: The Chilean Waiting List Corpus: a new resource for Clinical Named Entity Recognition.

Clinical NLP Workshop, EMNLP

Nov. 19 2020

Postdoctoral Bridge Scholarship

Biomedical Neuroscience Institute (BNI), University of Chile

Santiago, Chile

Sep. 2018

Scholarship for Internship Abroad

MECESUP Program Uch1304, University of Chile

Santiago, Chile

Jul. 2015

CONICYT National PhD Scholarship for Foreigners

Ministry of Education, Government of Chile

Santiago, Chile

Mar. 2013

Master’s approval with maximum distinction

Postgraduate School, University of Chile

Santiago, Chile

Jun. 2013

Ten best results at national level according to academic program: ECAES test

Ministry of Education, Republic of Colombia

Medellín, Colombia

2008